Paper Citing NAMD - Abstract
Hajjar, Eric; Korkmaz, Brice; Reuter, Nathalie
Differences in the substrate binding sites of murine and human proteinase 3 and neutrophil elastase
FEBS LETTERS, 581:5685-5690, DEC 11 2007
Understanding the differences between murine (m) and human (h) proteinase 3 (PR3) and neutrophil elastase (NE) is crucial for the interpretation of in vivo studies of inflammatory processes. We built structural models of mPR3 and mNE and analyzed their surface properties. We performed molecular dynamics (MD) simulations on several enzyme-peptide complexes to investigate their interaction patterns. The analysis of trajectories confirms that murine and human complexes have different interaction patterns with peptidic substrates. We provide a map of the binding sites of the murine proteases and suggest sequence motifs that we predict to be specific for mPR3 or mNE. (c) 2007 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
